One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: dyads_m1_shift4 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m1_shift4 (dyads_m1) |
 |
|
|
; dyads_m1; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wwAATGATtrw
; Alignment reference
a 0 0 0 0 28 20 80 80 0 0 80 0 17 29 24
c 0 0 0 0 15 18 0 0 3 0 0 0 8 13 16
g 0 0 0 0 12 14 0 0 0 80 0 0 19 20 12
t 0 0 0 0 25 28 0 0 77 0 0 80 36 18 28
|